Chitosan nanocomposites as a nano-bio tool in phytopathogen control

Chitosan, an economically viable and versatile biopolymer, exhibits a wide array of advantageous physicochemical and biological properties. Chitosan nanocomposites, formed by the amalgamation of chitosan or chitosan nanoparticles with other nanoparticles or materials, have garnered extensive attention across agricultural, pharmaceutical, and biomedical domains. These nanocomposites have been rigorously investigated due to their diverse applications, notably in combatting plant pathogens. Their remarkable efficacy against phytopathogens has positioned them as a promising alternative to conventional chemical-based methods in phytopathogen control, thus exploring interest in sustainable agricultural practices with reduced reliance on chemical interventions. This review aims to highlight the anti-phytopathogenic activity of chitosan nanocomposites, emphasizing their potential in mitigating plant diseases. Additionally, it explores various synthesis methods for chitosan nanoparticles to enhance readers' understanding. Furthermore, the analysis delves into elucidating the intricate mechanisms governing the antimicrobial effectiveness of these composites against bacterial and fungal phytopathogens.

Bacterial etiology of community-acquired pneumonia among adult patients in Ethiopia: A systematic review and meta-analysis

Background and objective

According to the Global Burden of Diseases, Injuries, and Risk Factors, lower respiratory infections cause more than 2.3 million deaths globally, with a majority occurring in sub-Saharan Africa, including Ethiopia.Community-acquired pneumonia (CAP) is a major contributor to global mortality and morbidity. Understanding the prevalence and common bacterial causes of CAP is crucial for clinicians to accurately diagnose and improve patient satisfaction. The purpose of this systematic review was to report the pooled prevalence and common bacterial etiologies of CAP among adult patients in Ethiopia.

Methods

This review was conducted based on the Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) guidelines. A comprehensive search of the published articles between January 2000 and October 2022 was performed using open access electronic databases such as PUBMED, Science Direct, CINAHL, HINARI, Google Scholar, and local university repositories. Cochrane Q and I2 values were used to assess heterogeneity among the studies. Publication bias was assessed using funnel plots and Egger's test. The random-effects model was used to estimate the pooled prevalence.

Results and conclusions

Of all the publications that were thoroughly searched, 9 studies with 2496 participants met the criteria for analysis. All of the studies were cross-sectionally designed and most of the studies used convenient sampling techniques. The included studies consisted of two conducted among adult patients diagnosed with CAP and living with HIV/AIDS, while the remaining seven studies were conducted among adult patients diagnosed with CAP without HIV/AIDS. The combined prevalence of bacterial causes of community-acquired pneumonia (CAP) among adult patients was found to be 39.18% (CI 36.34-42.02), with an I2 of 52.6 and a P value of 0.032. The primary bacterial cause was Klebsiella pneumoniae (9.1%), followed by Streptococcus pneumoniae (8.11%), and Staphylococcus aureus (6.8%). Therefore, it is advisable to introduce a diagnostic tool for identifying specific causative agents and drug resistance, which could lead to improved treatment and better patient outcomes by reducing the need for empirical treatments.

Variations in antibiotic resistomes associated with archaeal, bacterial, and viral communities affected by integrated rice-fish farming in the paddy field ecosystem

Antibiotic resistance genes (ARGs) serving as a newly recognized pollutant that poses potential risks to global human health, which in the paddy soil can be potentially altered by different agricultural production patterns. To elucidate the impacts and mechanisms of the widely used and sustainable agricultural production pattern, namely integrated rice-fish farming, on the antibiotic resistomes, we applied metagenomic sequencing to assess ARGs, mobile genetic elements (MGEs), bacteria, archaea, and viruses in paddy soil. There were 20 types and 359 subtypes of ARGs identified in paddy soil. The integrated rice-fish farming reduced the ARG and MGE diversities and the abundances of dominant ARGs and MGEs. Significantly decreased ARGs were mainly antibiotic deactivation and regulator types and primarily ranked level IV based on their potential threat to human health. The integrated rice-fish farming decreased the alpha diversities and altered microbial community compositions. MGEs, bacteria, archaea, and virus exhibited significant correlations with ARGs, while integrated rice-fish farming effectively changed their interrelationships. Viruses, bacteria, and MGEs played crucial roles in affecting the ARGs by the integrated rice-fish farming. The most crucial pathway by which integrated rice-fish farming affected ARGs was through the modulation of viral communities, thereby directly or indirectly influencing ARG abundance. Our research contributed to the control and restoration of ARGs pollution from a new perspective and providing theoretical support for the development of clean and sustainable agricultural production.

Prognosis of spontaneous bacterial peritonitis in patients with hepatocellular carcinoma

BACKGROUND

Hepatocellular carcinoma (HCC) is the fourth leading cause of death from cancer worldwide. Spontaneous bacterial peritonitis (SBP) is associated with poor prognosis. This study aimed to evaluate risk factors, differences in clinical characteristics and prognosis of SBP in patients with HCC in comparison with non-HCC patients.

METHODS

This study was conducted on patients with cirrhosis who were admitted to hospital with SBP. The patients were divided into two groups: SBP group with HCC (n = 150) and SBP group without HCC (n = 250).

RESULTS

Men and women accounted for 72% and 28% (n = 108 and 42, respectively) of the population in SBP group with HCC with mean age 55.8 ± 13.1 years. They accounted for 68.4% and 31.6% (n = 171 and 79, respectively) in the SBP group without HCC with mean age 56.8 ± 10.5 years. In-hospital mortality was 25.3% in the SBP group with HCC and 18.8% in SBP group without HCC. Gastrointestinal bleeding was the most common cause of death in both groups. No significant difference was observed in patient outcomes between the two studied groups. The deceased patients had significantly higher levels of leukocytes and neutrophils in ascitic fluid as well as a higher frequency of positive culture results than in patients who survived (p < 0.001). However, there was no significant difference in protein level in ascitic fluid or causative organism between patients who survived and those who died (p = 0.63 and 0.19, respectively).

CONCLUSIONS

Prognosis of SBP in patients with HCC seemed similar to that in patients without HCC.

Distinguishing community-acquired bacterial and viral meningitis: Microbes and biomarkers

Diagnostic tools to differentiate between community-acquired bacterial and viral meningitis are essential to target the potentially lifesaving antibiotic treatment to those at greatest risk and concurrently spare patients with viral meningitis from the disadvantages of antibiotics. In addition, excluding bacterial meningitis and thus decreasing antibiotic consumption would be important to help reduce antimicrobial resistance and healthcare expenses. The available diagnostic laboratory tests for differentiating bacterial and viral meningitis can be divided microbiological pathogen-focussed methods and biomarkers of the host response. Bacterial culture-independent microbiological methods, such as highly multiplexed nucleic acid amplification tests, are rapidly making their way into the clinical practice. At the same time, more conventional host protein biomarkers, such as procalcitonin and C-reactive protein, are supplemented by newer proteomic and transcriptomic signatures. This review aims to summarise the current state and the recent advances in diagnostic methods to differentiate bacterial from viral meningitis.

Prokaryote-derived phosphorylated Tau epitope vaccine is immunogenic and non-T-cell activated in the mice model

Accumulation of phosphorylated Tau protein is a prominent pathological hallmark of Alzheimer's disease (AD). However, current vaccines targeting phosphorylation sites are primarily modified using chemical reactions, which exhibit low efficiency in terms of linking to the vaccine carrier. Despite the identification of over 2000 phosphorylation sites on approximately 20% of E. coli proteins through proteomic studies, it remains unclear whether recombinant Tau proteins expressed in bacteria undergo direct phosphorylation. Additionally, limited information is available regarding the immunogenicity and safety profiles of prokaryotic-derived pTau epitope vaccines. Our study discovered that the prokaryotic system can induce phosphorylation on four residues (T181, T205, S262, and S396) of the full-length Tau protein. Based on this finding, we developed a prokaryotic-modified phosphorylated Tau protein vaccine and immunized wild-type mice, resulting in enhanced immunogenicity and a favorable safety profile.

PRFect: a tool to predict programmed ribosomal frameshifts in prokaryotic and viral genomes

BACKGROUND

One of the stranger phenomena that can occur during gene translation is where, as a ribosome reads along the mRNA, various cellular and molecular properties contribute to stalling the ribosome on a slippery sequence and shifting the ribosome into one of the other two alternate reading frames. The alternate frame has different codons, so different amino acids are added to the peptide chain. More importantly, the original stop codon is no longer in-frame, so the ribosome can bypass the stop codon and continue to translate the codons past it. This produces a longer version of the protein, a fusion of the original in-frame amino acids, followed by all the alternate frame amino acids. There is currently no automated software to predict the occurrence of these programmed ribosomal frameshifts (PRF), and they are currently only identified by manual curation.

RESULTS

Here we present PRFect, an innovative machine-learning method for the detection and prediction of PRFs in coding genes of various types. PRFect combines advanced machine learning techniques with the integration of multiple complex cellular properties, such as secondary structure, codon usage, ribosomal binding site interference, direction, and slippery site motif. Calculating and incorporating these diverse properties posed significant challenges, but through extensive research and development, we have achieved a user-friendly approach. The code for PRFect is freely available, open-source, and can be easily installed via a single command in the terminal. Our comprehensive evaluations on diverse organisms, including bacteria, archaea, and phages, demonstrate PRFect's strong performance, achieving high sensitivity, specificity, and an accuracy exceeding 90%. The code for PRFect is freely available and installs with a single terminal command.

CONCLUSION

PRFect represents a significant advancement in the field of PRF detection and prediction, offering a powerful tool for researchers and scientists to unravel the intricacies of programmed ribosomal frameshifting in coding genes.

Streptococcus pyogenes Meningitis in a Pediatric Patient: Case Report

Streptococcus pyogenes causes a wide spectrum of diseases in children. However, meningitis due to this pathogen is highly uncommon. Although rare, it is associated with a high case fatality rate and can result in severe neurological sequelae. We report a case of Streptococcus pyogenes meningitis in a previously healthy 3-year-old boy. The purpose of this case report is to emphasize that this agent should be considered a cause of meningitis in previously healthy infants because of its frequent association with complications, sequelae, and high mortality rates.

Antibiotic susceptibility and genotypic characterization of Neisseria gonorrhoeae isolates in the Comunidad Valenciana (Spain): GONOvig project

INTRODUCTION

The increase in sexually transmitted infections (STI) caused by Neisseria gonorrhoeae (NG) worldwide, together with the decrease in antibiotic susceptibility, forced us to understand the epidemiology of gonococcal infection.

METHODS

The GONOvig project analyzed, comparatively following CLSI and EUCAST criteria, the antibiotic susceptibility of 227 NG strains collected in thirteen representative hospitals of the Valencia Community (CV) between 2013 and 2018. Additionally, molecular typing of 175 strains using the NG multi-antigen sequence typing technique (NG-MAST) was performed.

RESULTS

High rates of resistance to tetracycline (38.2% by CLSI and 50.9% by EUCAST) and ciprofloxacin (49.1% CLSI and 54% EUCAST), and low percentages of resistance to spectinomycin (0%), cefixime (0.5% CLSI but 5.9% EUCAST), and ceftriaxone (1.5% CLSI and 2.4% EUCAST) were detected. Azithromycin resistance was 6% (both CLSI and EUCAST). Molecular analysis revealed the presence of 86 different sequence types (ST), highlighting ST2992 (7.4%), ST3378 (6.9%), ST2400 (4.6%) and ST13288 (6.9%), which was associated with resistance to cefixime (P=.031). The main genogroups (G) were G1407 (13.1%), G2992 (10.3%), G2400 (6.3%) and G387 (3.4%). G1407 and G2400 were associated with resistance to ciprofloxacin (P<.03).

CONCLUSION

Low resistance to ceftriaxone, a worrying resistance to azithromycin and a wide variety of circulating sequence types have been detected, some of which show correlation with certain resistance profiles.

Optimizing QoS and security in agriculture IoT deployments: A bioinspired Q-learning model with customized shards

Agriculture Internet of Things (AIoTs) deployments require design of high-efficiency Quality of Service (QoS) & security models that can provide stable network performance even under large-scale communication requests. Existing security models that use blockchains are either highly complex or require large delays & have higher energy consumption for larger networks. Moreover, the efficiency of these models depends directly on consensus-efficiency & miner-efficiency, which restricts their scalability under real-time scenarios. To overcome these limitations, this study proposes the design of an efficient Q-Learning bioinspired model for enhancing QoS of AIoT deployments via customized shards. The model initially collects temporal information about the deployed AIoT Nodes, and continuously updates individual recurring trust metrics. These trust metrics are used by a Q-Learning process for identification of miners that can participate in the block-addition process. The blocks are added via a novel Proof-of-Performance (PoP) based consensus model, which uses a dynamic consensus function that is based on temporal performance of miner nodes. The PoP consensus is facilitated via customized shards, wherein each shard is deployed based on its context of deployment, that decides the shard-length, hashing model used for the shard, and encryption technique used by these shards. This is facilitated by a Mayfly Optimization (MO) Model that uses PoP scores for selecting shard configurations. These shards are further segregated into smaller shards via a Bacterial Foraging Optimization (BFO) Model, which assists in identification of optimal shard length for underlying deployment contexts. Due to these optimizations, the model is able to improve the speed of mining by 4.5%, while reducing energy needed for mining by 10.4%, improving the throughput during AIoT communications by 8.3%, and improving the packet delivery consistency by 2.5% when compared with existing blockchain-based AIoT deployment models under similar scenarios. This performance was observed to be consistent even under large-scale attacks.

An analysis of differences in Carbapenem-resistant Enterobacterales in different regions: a multicenter cross-sectional study

OBJECTIVE

This study aimed to explore the characteristics of carbapenem-resistant Enterobacterales (CRE) patients in the intensive care unit (ICU) in different regions of Henan Province to provide evidence for the targeted prevention and treatment of CRE.

METHODS

This was a cross-sectional study. CRE screening was conducted in the ICUs of 78 hospitals in Henan Province, China, on March 10, 2021. The patients were divided into provincial capital hospitals and nonprovincial capital hospitals for comparative analysis.

RESULTS

This study involved 1009 patients in total, of whom 241 were CRE-positive patients, 92 were in the provincial capital hospital and 149 were in the nonprovincial capital hospital. Provincial capital hospitals had a higher rate of CRE positivity, and there was a significant difference in the rate of CRE positivity between the two groups. The body temperature; immunosuppressed state; transfer from the ICU to other hospitals; and use of enemas, arterial catheters, carbapenems, or tigecycline at the provincial capital hospital were greater than those at the nonprovincial capital hospital (P < 0.05). However, there was no significant difference in the distribution of carbapenemase strains or enzymes between the two groups.

CONCLUSIONS

The detection rate of CRE was significantly greater in provincial capital hospitals than in nonprovincial capital hospitals. The source of the patients, invasive procedures, and use of advanced antibiotics may account for the differences. Carbapenem-resistant Klebsiella pneumoniae (CR-KPN) was the most prevalent strain. Klebsiella pneumoniae carbapenemase (KPC) was the predominant carbapenemase enzyme. The distributions of carbapenemase strains and enzymes were similar in different regions.

Metagenomic assembly is the main bottleneck in the identification of mobile genetic elements

Antimicrobial resistance genes (ARG) are commonly found on acquired mobile genetic elements (MGEs) such as plasmids or transposons. Understanding the spread of resistance genes associated with mobile elements (mARGs) across different hosts and environments requires linking ARGs to the existing mobile reservoir within bacterial communities. However, reconstructing mARGs in metagenomic data from diverse ecosystems poses computational challenges, including genome fragment reconstruction (assembly), high-throughput annotation of MGEs, and identification of their association with ARGs. Recently, several bioinformatics tools have been developed to identify assembled fragments of plasmids, phages, and insertion sequence (IS) elements in metagenomic data. These methods can help in understanding the dissemination of mARGs. To streamline the process of identifying mARGs in multiple samples, we combined these tools in an automated high-throughput open-source pipeline, MetaMobilePicker, that identifies ARGs associated with plasmids, IS elements and phages, starting from short metagenomic sequencing reads. This pipeline was used to identify these three elements on a simplified simulated metagenome dataset, comprising whole genome sequences from seven clinically relevant bacterial species containing 55 ARGs, nine plasmids and five phages. The results demonstrated moderate precision for the identification of plasmids (0.57) and phages (0.71), and moderate sensitivity of identification of IS elements (0.58) and ARGs (0.70). In this study, we aim to assess the main causes of this moderate performance of the MGE prediction tools in a comprehensive manner. We conducted a systematic benchmark, considering metagenomic read coverage, contig length cutoffs and investigating the performance of the classification algorithms. Our analysis revealed that the metagenomic assembly process is the primary bottleneck when linking ARGs to identified MGEs in short-read metagenomics sequencing experiments rather than ARGs and MGEs identification by the different tools.

Bacterial colonisation of surface and core of palatine tonsils among Tanzanian children with recurrent chronic tonsillitis and obstructive sleep apnoea who underwent (adeno)tonsillectomy

OBJECTIVE

Acute and chronic tonsillitis are frequently treated with antibiotics. This study aimed to understand the presence of pathogenic micro-organisms on the surface and core of chronically infected tonsils among Tanzanian children.

METHODS

The study enrolled children undergoing adenotonsillectomy. Surface and core tonsillar swabs were taken. Quantitative polymerase chain reaction was performed for Streptococcus pneumoniae, Haemophilus influenzae, Moraxella catarrhalis, Staphylococcus aureus, Neisseria meningitidis and Pseudomonas aeruginosa.

RESULTS

Surface and core combined, isolated N meningitidis (86.1 per cent) was found the most, followed by H influenzae (74.9 per cent), S pneumoniae (42.6 per cent) and S aureus (28.7 per cent). M catarrhalis and P aeruginosa were only found in a few patients, 5.6 per cent and 0.8 per cent respectively.

CONCLUSION

Colonisation of the tonsillar surface and core has been found. Potentially pathogenic micro-organisms are likely to be missed based on a throat swab. Hence, the practice of surface tonsillar swabbing may be misleading or insufficient.

The Application of Bacteriophage and Photoacoustic Flow Cytometry in Bacterial Identification

Infection with resistant bacteria has become an ever-increasing problem in modern medical practice. Bacteremia is a serious and potentially lethal condition that can lead to sepsis without early intervention. Currently, broad-spectrum antibiotics are prescribed until bacteria can be identified through blood cultures, a process that can take 2-3 days and is unable to provide quantitative information. Staphylococcus aureus (S. aureus) is a leading cause of bacteremia, and methicillin-resistant S. aureus (MRSA) accounts for more than a third of the cases. Other bacteria such as Clostridium difficile, Acinetobacter baumannii, and Carbapenem-resistant Enterobacteriaceae are becoming more prevalent and antibiotic-resistant. Rapid diagnostics for each of these superbugs has been a priority for health organizations around the world. Bacteriophages have evolved for millions of years to develop exquisite specificity in target binding using their host attachment proteins. Bacteriophages are viruses that infect bacteria. Bacteriophages use tail spikes, specialized attachment proteins, to bind specifically to their target bacterial cell surface proteins. We use bacteriophages and parts of bacteriophages as specific tags coupled with photoacoustic flow cytometry for the detection and quantification of bacteria. In photoacoustic flow cytometry, laser light is absorbed by particles under flow, and the ultrasound waves generated on the release of the energy are detected. Photoacoustics involves the detection of ultrasound waves resulting from laser irradiation. In photoacoustic flow cytometry, pulsed laser light is delivered to a sample flowing past a focused transducer, and particles that absorb laser light create a photoacoustic response. Bacteria can be tagged with dyed bacteriophage and processed through a photoacoustic flow cytometer where they are detected by the acoustic response. In this chapter, we describe the procedure and methods used to accomplish this. Often the limiting factor for the treatment of patients is the time spent waiting for results. It is our hope that the work presented in this chapter can be a foundation for future work and provide an ability to detect bacterial pathogens in blood cultures. Bacterial plate cultures and Gram staining are nineteenth-century technologies that have been the gold standards for decades, but current trends in resistant bacteria have necessitated a move toward more rapid and quantifiable diagnostic tools.

Retrofitting of concrete for rigid pavement using bacterial: A meta-analysis

Cracking in tension causes damage to regular concrete. When the surface of the concrete cracks, liquids can enter and damage the structure. Remediating concrete in rigid pavements is time-consuming, costly, and challenging. Concrete cracking can be reduced using sustainable solutions, such as concrete bacteria. Using concrete bacteria is an innovative method for continuously retrofitting concrete, improving its durability, and reducing maintenance costs. Several studies have explored the possibilities of a wide range of bacteria and demonstrated concrete retrofitting. However, in these extensive studies of sustainable solutions, the role of concrete bacteria in retrofitting concrete for rigid pavement has not been clarified. This meta-analysis aims to compare and contrast the performance of various microorganisms in concrete restoration, considering the bacteria concentration, total concrete components, and water/cement ratio. Data from 371 articles were entered into the initial database and 37 articles into the final database for meta-analysis. Low concentrations (10 CFU/mL) of Bacillus subtilis increased the compressive strength after 28 days at 46.8 MPa, and the optimum concentration of Bacillus subtilis was 105 CFU/mL, resulting in an optimum compressive strength of 58.2 MPa after 28 days, an optimum water/cement ratio of 0.3, and the optimum total ingredients (cement, fine and coarse aggregates) ranging from 2000 to 2400 kg/m3. This meta-analysis study supports a new approach to selecting concrete bacteria and developing sustainable advances in concrete technology.

New lignan glycosides from Justicia secunda Vahl (Acanthaceae) with antimicrobial and antiparasitic properties

Three new lignan glucosides, namely, justisecundosides A (1), B (2a), and C (2b), were isolated from the whole plant of Justicia secunda together with seven known compounds (3-9). Their structures were established based on a comprehensive analysis of HR-ESI-MS, IR, UV, and CD, in conjunction with their 1D and 2D-NMR data. A putative biogenetic pathway of compounds 1-2a,b from coniferyl alcohol was proposed. In addition, the antimicrobialactivities of the extract, fractions, and some isolated compounds were assessed against multiresistant bacterial and fungal strains. Furthermore, the antiplasmodial, antileishmanial, and antitrypanosomal activities were assessed against the sensitive (3D7) and multidrug-resistant (Dd2) strains of P. falciparum, promastigote and bloodstream forms of L. donovani, and Trypanosoma brucei, respectively. Compound 4 exhibited moderate antibacterial activity against Staphylococcus aureus SA RN 46003 with a MIC value of 62.5 μg/mL. Besides, compound 6 demonstrated a very good activity against sensitive (IC50Pf3D7: 0.81 μg/mL) and multidrug-resistant (IC50PfDd2: 14.61 μg/mL) strains of P. falciparum while compound 4 displayed good antitrypanosomal activity (IC50: 1.19 μg/mL). Also, compound 1 was the most active on the promastigote form of L. donovani with an IC50 of 13.02 μg/mL.

Diagnostic utility of procalcitonin for bacterial infections in diabetic ketoacidosis

Procalcitonin is a widely used infection biomarker; however, its utility in identifying bacterial infection in diabetic ketoacidosis (DKA) is unclear. We aimed to evaluate its diagnostic performance for detecting DKA cases triggered by bacterial infections. We reviewed 303 case records of patients aged ≥ 13 years with DKA admitted to the emergency department, PGIMER (Chandigarh), between 2017 and 2022. Baseline procalcitonin was measured by electrochemiluminescence immunoassay, and a value > 0.5 ng/mL was considered elevated. Both microbiological reference standard (MRS) and composite reference standard (CRS) were used to evaluate the diagnostic performance of procalcitonin. 151/303 (49.8%) DKA cases had infection precipitations. Bacterial infections were present in 98 patients (53 microbiologically confirmed), of which urinary tract infection (n = 42), pneumonia (n = 19), skin and soft-tissue infection (n = 13), and bacteremia (n = 11) were common. The median value of procalcitonin was higher with bacterial infections than in patients without (3.68 vs. 1.00, P-value < 0.001). An elevated procalcitonin to detect bacterial infections in DKA had sensitivity 84.69%, specificity 34.15%, positive likelihood ratio (LR +) 1.29, and negative likelihood ratio (LR -) 2.44, against CRS. Against MRS, both LR + and LR - further decreased to 1.23 and 1.81, respectively. Using the receiver-operating-characteristic curve, an optimal cut-off of procalcitonin was calculated at 1.775 ng/ml against both CRS (area under curve 0.655, sensitivity 68.37%, specificity 59.02%, LR + 1.67, LR - 1.86, Yoden's index 0.274) and MRS (area under curve 0.616, sensitivity 67.92%, specificity 59.02%, LR + 1.66, LR - 1.84, Yoden's index 0.269). Procalcitonin does not help detect bacterial infections in patients with DKA at admission.

Epidemiology and clinical characteristics of severe acute respiratory infections among hospitalized children under 5 years of age in a tertiary care center in Bangkok, Thailand, 2019-2020

Background

Acute respiratory infections (ARIs) are common in children and can range in severity from mild self-limiting illnesses to more severe conditions such as pneumonia and respiratory failure. Data on the epidemiology of viral and bacterial pathogens causing ARIs in children are scarce in this region. This study aimed to investigate the epidemiology and clinical manifestations of pathogens in children aged ≤5 years presenting with severe acute respiratory infection (SARI) in Bangkok, Thailand. The impact of rapid multiplex PCR-based testing on clinical management is also explored.

Methods

This cross-sectional study enrolled consecutive children aged ≤5 years presenting with SARI at a tertiary care centre in Bangkok, Thailand, between 2019 and 2020. Nasopharyngeal swabs were collected once at admission, and viral and bacterial pathogens were tested using the QIAstat-Dx respiratory panel.

Results

A total of 169 children were enrolled in this study. At least one pathogenic virus was detected in 91.7 % of participants. Based on the final diagnoses made upon discharge, 30.2 % had upper respiratory tract infection, whereas 66.3 % had lower respiratory tract infection. Pneumonia was the most common diagnosis (59.2 %). The most common pathogen identified was rhino/enterovirus (45.2 %), followed by respiratory syncytial virus (31.6 %) and parainfluenza virus (14.2 %). Co-infection was found in 15.4 % and was not associated with increased disease severity.

Conclusions

This study provides additional insights into the pathogen profiles, clinical diagnosis, and co-infection combinations of ARIs in hospitalized children. This information is useful for diagnosis and treatment of ARIs, as well as implementation of appropriate infection control measures and guidance for future vaccine policy development.

Pneumonia pattern recognition on ultra-low-dose CT does not allow for a reliable differentiation between viral and bacterial pneumonia: A multicentre observer study

PURPOSE

While a reliable differentiation between viral and bacterial pneumonia is not possible with chest X-ray, this study investigates whether ultra-low-dose chest-CT (ULDCT) could be used for this purpose.

METHODS

In the OPTIMACT trial 281 patients had a final diagnosis of pneumonia, and 96/281 (34%) had one or more positive microbiology results: 60 patients viral pathogens, 48 patients bacterial pathogens. These 96 ULDCT's were blindly and independently evaluated by two chest radiologists, who reported CT findings, pneumonia pattern, and most likely type of pathogen. Differences between groups were analysed for each radiologist separately, diagnostic accuracy was evaluated by calculating sensitivity.

RESULTS

The dominant CT finding significantly differed between the viral and bacterial pathogen groups (p = 0.04; p = 0.04). Consolidation was the most frequent dominant CT finding in both patients with viral and bacterial pathogens, but was observed significantly more often in those with a bacterial pathogen: 32/60 and 22/60 versus 38/48 and 31/48 (p = 0.005; p = 0.004). The lobar pneumonia pattern was more frequently observed in patients with a bacterial pathogen: 23/48 and 18/48, versus 10/60 and 8/60 for viral pathogens (p < 0.001; p = 0.004). For the bronchopneumonia and interstitial pneumonia patterns the proportions of viral and bacterial pathogens were not significantly different. Both radiologists suggested a viral pathogen correctly (sensitivity) in 6/60 (10%), for a bacterial pathogen this was 34/48 (71%).

CONCLUSION

Reliable differentiation between viral and bacterial pneumonia could not be made by pattern recognition on ULDCT, although a lobar pneumonia pattern was significantly more often observed in bacterial infection.

An Overview of Acute Otitis Externa

Acute otitis externa, cellulitis of the external auditory canal, is most frequently due to bacteria. Patients may present with otalgia, aural fullness, hearing loss, and otorrhea. Its diagnosis is a clinical one. Treatment is focused on analgesia, treating the underlying infection and preventing recurrence.

Relationship between molecular pathogen detection and clinical disease in febrile children across Europe: a multicentre, prospective observational study

BACKGROUND

The PERFORM study aimed to understand causes of febrile childhood illness by comparing molecular pathogen detection with current clinical practice.

METHODS

Febrile children and controls were recruited on presentation to hospital in 9 European countries 2016-2020. Each child was assigned a standardized diagnostic category based on retrospective review of local clinical and microbiological data. Subsequently, centralised molecular tests (CMTs) for 19 respiratory and 27 blood pathogens were performed.

FINDINGS

Of 4611 febrile children, 643 (14%) were classified as definite bacterial infection (DB), 491 (11%) as definite viral infection (DV), and 3477 (75%) had uncertain aetiology. 1061 controls without infection were recruited. CMTs detected blood bacteria more frequently in DB than DV cases for N. meningitidis (OR: 3.37, 95% CI: 1.92-5.99), S. pneumoniae (OR: 3.89, 95% CI: 2.07-7.59), Group A streptococcus (OR 2.73, 95% CI 1.13-6.09) and E. coli (OR 2.7, 95% CI 1.02-6.71). Respiratory viruses were more common in febrile children than controls, but only influenza A (OR 0.24, 95% CI 0.11-0.46), influenza B (OR 0.12, 95% CI 0.02-0.37) and RSV (OR 0.16, 95% CI: 0.06-0.36) were less common in DB than DV cases. Of 16 blood viruses, enterovirus (OR 0.43, 95% CI 0.23-0.72) and EBV (OR 0.71, 95% CI 0.56-0.90) were detected less often in DB than DV cases. Combined local diagnostics and CMTs respectively detected blood viruses and respiratory viruses in 360 (56%) and 161 (25%) of DB cases, and virus detection ruled-out bacterial infection poorly, with predictive values of 0.64 and 0.68 respectively.

INTERPRETATION

Most febrile children cannot be conclusively defined as having bacterial or viral infection when molecular tests supplement conventional approaches. Viruses are detected in most patients with bacterial infections, and the clinical value of individual pathogen detection in determining treatment is low. New approaches are needed to help determine which febrile children require antibiotics.

FUNDING

EU Horizon 2020 grant 668303.

Endogenous Endophthalmitis - A Major Review

Endogenous endophthalmitis (EE) is an uncommon but potentially devastating ocular infection involving the inner layers of the eye. The global incidence of EE is on the rise. Common ocular signs and symptoms associated with EE include conjunctival injection, ocular pain, and reduced visual acuity. On clinical examination, a history of prior or coexisting systemic infections, symptoms (e.g., fever, malaise), and localizing features may be noted. Clinical diagnosis is often challenging, resulting in critical delays that contribute to a poor prognosis. Blood cultures and ocular fluid samples can aid in conforming causative pathogen(s), after which empirical antibiotic therapy, both systemic and intravitreal, should be instated. The use of steroids to suppress inflammation remains controversial. Surgical options include pars plana vitrectomy. Overall prognosis varies depending on host and pathogen factors, and early diagnosis and initiation of appropriate treatment are crucial.

First Report of Salmonella Serovar Typhimurium and Monophasic Typhimurium Clinical Isolates Harboring mcr-9 in Portugal

N/a.

Bacterial etiology, antimicrobial resistance and factors associated with community acquired pneumonia among adult hospitalized patients in Southwest Ethiopia

Background and Objectives

Antibiotic resistance is a significant problem that restricts the options for treating bacterial pneumonia. This research aimed to determine the bacterial causes of pneumonia and antibiotic resistance among hospitalized patients in southwest Ethiopia.

Materials and Methods

We collected and analyzed 150 sputum samples from individuals with community-acquired pneumonia from April 1st to October 30th, 2019. Standard bacteriological procedures were used to identify the bacteria. Kirby Bauer's disk diffusion method was used to assess the bacteria's susceptibility patterns. Production of carbapenemase and extended-spectrum-lactamase were confirmed phenotypically. Odds ratios and the chi-square test were computed.

Results

On the whole, bacterial pathogens were verified in 50% of the sputum samples. The predominant bacterial isolates were Klebsiella species, followed by Pseudomonas aeruginosa, Staphylococcus aureus and Streptococcus pneumoniae. About 77.5% of isolates were multidrug resistant. Moreover, 40.5% and 10.8% of the isolates were ESBL and carbapenemase producers, respectively. Aging, tobacco smoking, previous history of pneumonia, heart disease, and chronic respiratory disease had association with sputum culture-positivity.

Conclusion

As a result, it is important to regularly monitor the bacterial etiologies and their patterns of resistance. Additionally, sociodemographic and clinical characteristics should all be taken into account while managing patients with pneumonia empirically in this context.

Bacterial orbital cellulitis - A review

Infections of orbit and periorbita are frequent, leading to significant morbidity. Orbital cellulitis is more common in children and young adults. At any age, infection from the neighboring ethmoid sinuses is a likely cause and is thought to result from anatomical characteristics like thin medial wall, lack of lymphatics, orbital foramina, and septic thrombophlebitis of the valveless veins between the two. Other causes are trauma, orbital foreign bodies, preexisting dental infections, dental procedures, maxillofacial surgeries, Open Reduction and Internal Fixation (ORIF), and retinal buckling procedures. The septum is a natural barrier to the passage of microorganisms. Orbital infections are caused by Gram-positive, Gram-negative organisms and anaerobes in adults and in children, usually by Staphylococcus aureus or Streptococcus species. Individuals older than 15 years of age are more likely to harbor polymicrobial infections. Signs include diffuse lid edema with or without erythema, chemosis, proptosis, and ophthalmoplegia. It is an ocular emergency requiring admission, intravenous antibiotics, and sometimes surgical intervention. Computed tomography (CT) and magnetic resonance imaging (MRI) are the main modalities to identify the extent, route of spread from adjacent structures, and poor response to intravenous antibiotics and to confirm the presence of complications. If orbital cellulitis is secondary to sinus infection, drainage of pus and establishment of ventilation to the sinus are imperative. Loss of vision can occur due to orbital abscess, cavernous sinus thrombosis, optic neuritis, central retinal artery occlusion, and exposure keratopathy, and possible systemic sequelae include meningitis, intracranial abscess, osteomyelitis, and death. The article was written by authors after a thorough literature search in the PubMed-indexed journals.

Effects of genetic and environmental variables on biofilm development dynamics in Achromobacter mucicolens

Background and Objectives

The study aimed to investigate whether Achromobacter mucicolens IA strain biofilm formation, which contributes to antibiotic resistance, could be enhanced by readily available nutrient sources like carbohydrates and environmental factors such as pH and NaCl. Additionally, the study aimed to identify any inherent genes that support biofilm formation in this strain, which is an opportunistic pathogen that affects immunocompromised patients and is resistant to many antibiotics.

Materials and Methods

Biofilm growth in different carbohydrate, pH, and NaCl concentrated media was measured using crystal violet microtiter assay. All the treatments were subjected to biostatistics analysis for normality, Test of Homogeneity, one way ANOVA analysis. Whole-genome sequencing of our IA strain was conducted to identify various gene sequences.

Results

Biofilm formation was measured at different carbohydrate concentrations, and the optimum biofilm formation was observed at 3M glucose and 0.5M NaCl, while the lowest results were seen at 2M maltose concentration. Whole-genome sequencing identified potential genes involved in biofilm formation, pathogenicity, protein metabolism, flagellar motility, cell wall component synthesis, and a multidrug efflux pump.

Conclusion

These findings suggest that biofilm formation is influenced by extrinsic and intrinsic factors, which could aid in the development of effective treatments for resistant infections.

Advanced Nitric Oxide Generating Nanomedicine for Therapeutic Applications

Nitric oxide (NO), a gaseous transmitter extensively present in the human body, regulates vascular relaxation, immune response, inflammation, neurotransmission, and other crucial functions. Nitrite donors have been used clinically to treat angina, heart failure, pulmonary hypertension, and erectile dysfunction. Based on NO's vast biological functions, it further can treat tumors, bacteria/biofilms and other infections, wound healing, eye diseases, and osteoporosis. However, delivering NO is challenging due to uncontrolled blood circulation release and a half-life of under five seconds. With advanced biotechnology and the development of nanomedicine, NO donors packaged with multifunctional nanocarriers by physically embedding or chemically conjugating have been reported to show improved therapeutic efficacy and reduced side effects. Herein, we review and discuss recent applications of NO nanomedicines, their therapeutic mechanisms, and the challenges of NO nanomedicines for future scientific studies and clinical applications. As NO enables the inhibition of the replication of DNA and RNA in infectious microbes, including COVID-19 coronaviruses and malaria parasites, we highlight the potential of NO nanomedicines for antipandemic efforts. This review aims to provide deep insights and practical hints into design strategies and applications of NO nanomedicines.

Immunomodulatory Activity of Probiotics in Models of Bacterial Infections

As resistance to conventional antibiotics among bacteria continues to increase, researchers are increasingly focusing on alternative strategies for preventing and treating bacterial infections, one of which is microbiota modulation. The objective of this review is to analyze the scientific literature on the immunomodulatory effects of probiotics in bacterial infections. This is an integrative review of the literature based on systematic steps, with searches performed in the databases Medline, PubMed, Scopus, Embase, and ScienceDirect. The most prevalent bacterial genera used to evaluate infectious processes were Salmonella, Escherichia, Klebsiella, and Streptococcus. Lactobacillus was the most commonly used probiotic genus, with Lactobacillus delbrueckii subsp. bulgaricus is the most frequently used species. In most studies, prophylactic treatment with concentrations of probiotics equal to or greater than 8 log CFU/mL was chosen. However, there was considerable heterogeneity in terms of effective treatment duration, indicating that the results cannot be generalized across all studies. This review found that probiotics interact with the immune system through different mechanisms and have a positive effect on preventing different types of bacterial infections.

Microbial community structure and antibiotic resistance profiles in sediments with long-term aquaculture history

The aim of this investigation was to examine the microbial populations and their resistance patterns towards antibiotics, including the impact of nitrogen metabolism in response to the reintroduction of antibiotics, as well as the presence of resistance genes in sediments from shrimp ponds that have been utilized for extended periods of 5, 15, and over 30 years. Results showed that the sediments exhibited a high prevalence of Proteobacteria, Bacteroidetes, Planctomycetes, Chloroflexi, and Oxyphotobacteria as the most abundant bacterial phyla, accounting for 70.35-77.43% of the total bacterial community. The five most abundant phyla of fungi detected in all sediments, namely Rozellomycota, Ascomycota, Aphelidiomycota, Basidiomycota, and Mortierellomycota, constituted 24.26-32.54% of the total fungal community. It was highly probable that the Proteobacteria and Bacteroidetes phyla serve as the primary reservoir of antibiotic-resistant bacteria (ARB) in the sediment, which included various genera like Sulfurovum, Woeseia, Sulfurimonas, Desulfosarcina, and Robiginitalea. Among these genera, Sulfurovum appeared to be the most widespread in the sediment of aquaculture ponds that have been in operation for more than three decades, while Woeseia dominated in ponds that have been recently reclaimed and have a 15-year aquaculture history. Antibiotic resistance genes (ARGs) were categorized into seven distinct groups according to their mechanism of action. The prevalence of multidrug-resistant ARGs was found to be the highest among all types, with an abundance ranging from 8.74 × 10^-2 to 1.90 × 10^-1 copies per 16S rRNA gene copies. The results of a comparative analysis of sediment samples with varying aquaculture histories indicated that the total relative abundance of ARGs was significantly diminished in sediment with a 15-year aquaculture history as opposed to sediment with either a 5-year or 30-year aquaculture history. Another assessment of antibiotic resistances in aquaculture sediments involved an examination of the effects of reintroducing antibiotics on nitrogen metabolism processes. The findings revealed that the rates of ammonification, nitrification, and denitrification in the sediment with a history of 5 years and 15 years, decreased as the concentration of oxytetracycline increased from 1 to 300, and 2000 mg/kg, and inhibitory effects were found to be less pronounced in sediments with a 5-year history compared to those with a 15-year history. In contrast, oxytetracycline exposure led to a significant decrease in the rates of these processes in aquaculture pond sediments with a >30 years of aquaculture history across all the concentrations tested. The emergence and dissemination of antibiotic resistance profiles in aquaculture environments requires attention in future aquaculture management.

Granulomatous lesion in the caruncle: Primary syphilitic lesion in a HIV male patient

Syphilis ocular manifestations can occur at any stage of the disease and involve almost any ocular structure. In this case report, we present a very rare conjunctival affectation that was the primary syphilitic lesion in a HIV-positive male patient. The diagnosis was supported by the serologic test, the dark-field microscopy of the lesion, and the exceptional treatment response.

Emerging role of bacterial outer membrane vesicle in gastrointestinal tract

Bacteria form a highly complex ecosystem in the gastrointestinal (GI) tract. In recent years, mounting evidence has shown that bacteria can release nanoscale phospholipid bilayer particles that encapsulate nucleic acids, proteins, lipids, and other molecules. Extracellular vesicles (EVs) are secreted by microorganisms and can transport a variety of important factors, such as virulence factors, antibiotics, HGT, and defensive factors produced by host eukaryotic cells. In addition, these EVs are vital in facilitating communication between microbiota and the host. Therefore, bacterial EVs play a crucial role in maintaining the GI tract's health and proper functioning. In this review, we outlined the structure and composition of bacterial EVs. Additionally, we highlighted the critical role that bacterial EVs play in immune regulation and in maintaining the balance of the gut microbiota. To further elucidate progress in the field of intestinal research and to provide a reference for future EV studies, we also discussed the clinical and pharmacological potential of bacterial EVs, as well as the necessary efforts required to understand the mechanisms of interaction between bacterial EVs and gut pathogenesis.

Distribution and the trend of airborne particles and bio-aerosol concentration in pediatric intensive care units with different ventilation setting at two hospitals in Riyadh, Saudi Arabia

OBJECTIVE

To examine the distribution and the trend of airborne particles and bio-aerosol concentration in pediatric intensive care units (PICUs) in two tertiary care hospitals with different ventilation setting.

METHODS

Hospitals A but not B is provided with a central HEPA filter. PICUs in both hospitals were categorized into protective environment (PE) with room HEPA filter, semi-protective environment (SPE) with portable air-purifier, and non-protective environment (NPE) with neither system. Fine particles (≤ 2.5 µm) and coarse particles (≤ 10.0 µm) were obtained using optical particle counter (Lighthouse Handheld 3016) and total bacterial (TBC) and fungal (TFC) counts were obtained using Andersen air sampler.

RESULTS

Hospital B had significantly higher levels of fine and coarse particles (in all room), TBC (in PE), but not TFC compared with matched rooms in hospital A. In hospital B, the levels of fine particles, coarse particles, and TBC were lowest in SPE (p < 0.001, p = 0.004, and p = 0.006, respectively) while TFC was lowest in NPE (p = 0.014). Airborne particles, TBC, and TFC had variable trends with some of the indoor peaks follow outdoor peaks. Gram-positive bacteria (69 %) were the predominant bacteria in hospital A while bacterial flora (70 %) were the predominant bacteria in hospital B (p < 0.001 for each).

CONCLUSIONS

The levels of airborne contaminants and microbial counts in PICUs are significantly affected by the ventilation system and to less extent by outdoor levels. The results indicated that advanced filtration system and central HEPA filters play a significant role in the reduction of indoor fine particulates and TBC.

Folding of heterologous proteins in bacterial cell factories: Cellular mechanisms and engineering strategies

The expression of correctly folded and functional heterologous proteins is important in many biotechnological production processes, whether it is enzymes, biopharmaceuticals or biosynthetic pathways for production of sustainable chemicals. For industrial applications, bacterial platform organisms, such as E. coli, are still broadly used due to the availability of tools and proven suitability at industrial scale. However, expression of heterologous proteins in these organisms can result in protein aggregation and low amounts of functional protein. This review provides an overview of the cellular mechanisms that can influence protein folding and expression, such as co-translational folding and assembly, chaperone binding, as well as protein quality control, across different model organisms. The knowledge of these mechanisms is then linked to different experimental methods that have been applied in order to improve functional heterologous protein folding, such as codon optimization, fusion tagging, chaperone co-production, as well as strain and protein engineering strategies.

Defining a clinical prediction rule to diagnose bacterial gastroenteritis requiring empirical antibiotics in an emergency department setting: A retrospective review

BACKGROUND

Gastroenteritis (GE) is a non-specific term for various pathologic states of the gastrointestinal tract. Infectious agents usually cause acute GE. At present, there are no robust decision-making rules that predict bacterial GE and dictate when to start antibiotics for patients suffering from acute GE to the emergency department (ED). We aim to define a clinical prediction rule to aid in the diagnosis of bacterial GE, requiring empirical antibiotics in adult patients presenting to the emergency department with acute GE.

METHODS

A two-year retrospective case review was performed on all cases from July 2015 to June 2017 that included patients with acute GE symptoms referred to the ED, after which their stool cultures were performed. The clinical parameters analyzed included patient with comorbid conditions, physical examination findings, historical markers, point-of-care and radiographic tests and other laboratory work. We then used multi-variate logistic regression analysis on each group (bacterial culture-positive GE and bacterial culture-negative GE) to elucidate clinical criteria with the highest yield for predicting bacterial gastroenteritis (BGE).

RESULTS

A total of 756 patients with a mean age of 52 years, 52% female and 48% male, respectively, were included in the study. On the basis of the data of these patients, we suggested using a scoring system to delineate the need for empirical antibiotics in patients with suspected bacterial GE based on six clinical and laboratory variables. We termed this the BGE score. A score 0 - 2 points suggests low risk (0.9%) of bacterial GE. A score of 3 - 4 points confers an intermediate risk of 12.0% and a score of 5 - 8 points confers a high risk of 85.7%. A cut-off of  ≥ 5 points may be used to predict culture-positive BGE with a 75% sensitivity and 75% specificity. The area under the receiver operating characteristic (AUROC) for the scoring system (range 0 - 8) was 0.812 (95% CI: 0.780-0.843) p-value < 0.001.

CONCLUSION

We suggest using the BGE scoring system (cut-off ≥ 5 points) to delineate the need for empirical antibiotics in patients diagnosed with gastroenteritis. While this is a pilot study, which will require further validation with a larger sample size, our proposed decision-making rule will potentially serve to improve the diagnosis of BGE and thus reduce unnecessary prescription of antibiotics, which will in turn reduce antibiotic-associated adverse events and save on costs worldwide.

Impact of multidrug resistance on the management of bacterial infections in cirrhosis

Patients with cirrhosis have an increased risk of infection and differently from other complications, that over the years are improving in their outcomes, infections in cirrhotic patients are still a major cause of hospitalization and death (up to 50% in-hospital mortality). Infections by multidrug-resistant organisms (MDRO) have become a major challenge in the management of cirrhotic patients with significant prognostic and cost-related impact. About one third of cirrhotic patients with bacterial infections is infected with MDR bacteria and their prevalence has increased in recent years. MDR infections have a worse prognosis compared to infections by non-resistant bacteria because they are associated with lower rate of infection resolution. An adequate management of cirrhotic patients with infections caused by MDR bacteria depends on the knowledge of some epidemiological aspects, such as the type of infection (spontaneous bacterial peritonitis, pneumonia, urinary tract infection and spontaneous bacteremia), bacteriological profile of antibiotic resistance at each health care unit and site of infection acquisition (community acquired, healthcare associated or nosocomial). Furthermore, regional variations in the prevalence of MDR infections determine that the choice of empirical antibiotic therapy must be adapted to the local microbiological epidemiology. Antibiotic treatment is the most effective measure to treat infections caused by MDRO. Therefore, optimizing antibiotic prescribing is critical to effectively treat these infections. Identification of risk factors for multidrug resistance is essential to define the best antibiotic treatment strategy in each case and the choice of an effective empirical antibiotic therapy and its early administration is cardinal to reduce mortality. On the other hand, the supply of new agents to treat these infections is very limited. Thus, specific protocols that include preventive measures must be implemented in order to limit the negative impact of this severe complication in cirrhotic patients.

The rhizosphere Microbiome of Malus sieversii (Ldb.) Roem. in the geographic and environmental gradients of China's Xinjiang

Malus sieversii (Ldb.) Roem. is the original species of modern cultivated apple and a key national essential conservation plant in China. In recent years, degradation and death of wild apple has been exacerbated by imbalances in the rhizosphere micro-ecosystems of wild apple forests due to soil nutrient loss, grazing, climate change and pest and disease outbreaks. However, the structure, diversity and response to environmental factors of wild apple rhizosphere microbial communities are so far unclear. In this study, the rhizosphere bacterial and eukaryotic communities of M. sieversii (Ldb.) Roem. in eight regions of the Yili River were analyzed using 16S/18S rDNA high-throughput sequencing technology. The results indicated that the bacterial operational taxonomic units (OTUs), Shannon index, and community composition were significantly lower in regions A, E, and F than in other regions. By contrast, the dominant eukaryotic communities in all regions were relatively similar in composition and differed less than the relative abundance of bacterial communities. Geographical and climatic distance were found to be key factors influencing the composition and diversity of wild apple rhizosphere microbial communities through mantel analysis. Moreover, these factors above were more correlated with bacterial diversity than with eukaryotes. This study identified the structure of wild apple rhizosphere microbial communities in Xinjiang and their interaction mechanisms under geographical and environmental gradients. It provides guidance for the sustainable management and ecological construction of wild apple forests in China.

No more tears from surgical site infections in interventional pain management

As the field of interventional pain management (IPM) grows, the risk of surgical site infections (SSIs) is increasing. SSI is defined as an infection of the incision or organ/space that occurs within one month after operation or three months after implantation. It is also common to find patients with suspected infection in an outpatient clinic. The most frequent IPM procedures are performed in the spine. Even though primary pyogenic spondylodiscitis via hematogenous spread is the most common type among spinal infections, secondary spinal infections from direct inoculation should be monitored after IPM procedures. Various preventive guidelines for SSI have been published. Cefazolin, followed by vancomycin, is the most commonly used surgical antibiotic prophylaxis in IPM. Diagnosis of SSI is confirmed by purulent discharge, isolation of causative organisms, pain/tenderness, swelling, redness, or heat, or diagnosis by a surgeon or attending physician. Inflammatory markers include traditional (C-reactive protein, erythrocyte sedimentation rate, and white blood cell count) and novel (procalcitonin, serum amyloid A, and presepsin) markers. Empirical antibiotic therapy is defined as the initial administration of antibiotics within at least 24 hours prior to the results of blood culture and antibiotic susceptibility testing. Definitive antibiotic therapy is initiated based on the above culture and testing. Combination antibiotic therapy for multidrug-resistant Gram-negative bacteria infections appears to be superior to monotherapy in mortality with the risk of increasing antibiotic resistance rates. The never-ending war between bacterial resistance and new antibiotics is continuing. This article reviews prevention, diagnosis, and treatment of infection in pain medicine.

Serotype Distribution and Antimicrobial Resistance of Streptococcus pneumoniae Causing Invasive Pneumococcal Disease in Korea Between 2017 and 2019 After Introduction of the 13-Valent Pneumococcal Conjugate Vaccine

Background

Streptococcus pneumoniae is a serious pathogen causing various infections in humans. We evaluated the serotype distribution and antimicrobial resistance of S. pneumoniae causing invasive pneumococcal disease (IPD) after introduction of pneumococcal conjugate vaccine (PCV)13 in Korea and investigated the epidemiological characteristics of multidrug-resistant (MDR) isolates.

Methods

S. pneumoniae isolates causing IPD were collected from 16 hospitals in Korea between 2017 and 2019. Serotyping was performed using modified sequential multiplex PCR and the Quellung reaction. Antimicrobial susceptibility tests were performed using the broth microdilution method. Multilocus sequence typing was performed on MDR isolates for epidemiological investigations.

Results

Among the 411 S. pneumoniae isolates analyzed, the most prevalent serotype was 3 (12.2%), followed by 10A (9.5%), 34 (7.3%), 19A (6.8%), 23A (6.3%), 22F (6.1%), 35B (5.8%), 11A (5.1%), and others (40.9%). The coverage rates of PCV7, PCV10, PCV13, and pneumococcal polysaccharide vaccine (PPSV)23 were 7.8%, 7.8%, 28.7%, and 59.4%, respectively. Resistance rates to penicillin, ceftriaxone, erythromycin, and levofloxacin were 13.1%, 9.2%, 80.3%, and 4.1%, respectively. MDR isolates accounted for 23.4% of all isolates. Serotypes 23A, 11A, 19A, and 15B accounted for the highest proportions of total isolates at 18.8%, 16.7%, 14.6%, and 8.3%, respectively. Sequence type (ST)166 (43.8%) and ST320 (12.5%) were common among MDR isolates.

Conclusions

Non-PCV13 serotypes are increasing among invasive S. pneumoniae strains causing IPD. Differences in antimicrobial resistance were found according to the specific serotype. Continuous monitoring of serotypes and antimicrobial resistance is necessary for the appropriate management of S. pneumoniae infections.

Molecular docking studies and biological evaluation of isoxazole-carboxamide derivatives as COX inhibitors and antimicrobial agents

Non-steroidal anti-inflammatory drugs (NSAIDs) are considered one of the most commonly used medications globally. Seventeen isoxazole-containing compounds with various functional groups were evaluated in this work to identify which one was the most potent and which group was most selective toward COX-1 and COX-2 by using an in vitro COX inhibition assay kit. Their cytotoxicity was evaluated on the normal hepatic cell line (LX-2) utilizing the MTS assay. Moreover, these molecules' antibacterial and antifungal activities were evaluated using a microdilution assay against several bacterial and fungal species. In addition, molecular docking studies were conducted to identify the possible binding interactions between these compounds and their biological targets by using the X-ray crystal structure of the human COX enzyme and different proteins of bacterial and fungal strains. At the same time, the QiKProp module was used for ADME-T analysis. The results showed that all evaluated isoxazole derivatives showed moderate to potent activities against COX enzymes. The most potent compound against COX-1 and COX-2 enzymes was A13, with IC50 values of 64 and 13 nM, respectively, and a significant selectivity ratio of 4.63. It was clear that the 3,4-dimethoxy substitution on the first phenyl ring and the Cl atom on the other phenyl pushed the 5-methyl-isoxazole ring toward the secondary binding pocket and created the ideal binding interactions with the COX-2 enzyme in comparison with the other compounds. Compound A8 showed antibacterial and antifungal activities against Pseudomonas aeruginosa, Klebsiella pneumonia, and Candida albicans with MIC values of 2 mg/ml. In fact, this compound showed possible binding interactions with the elastase in P. aeruginosa and KPC-2 carbapenemase in K. pneumonia. Furthermore, for better understanding, molecular dynamics simulations were undertaken to study the change in dynamicity of the protein backbone and ligand after the ligand binds to the protein and to ensure the stability of ligand-protein complexes.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-022-03408-8.

Characteristics, non-carcinogenic risk assessment and prediction by HYSPLIT of bioaerosol released from Hospital and Municipal Sewage, China

Bioaerosol is a new type of pollutant, which is related to the spread of many diseases. In particular, the bioaerosol produced in the hospital sewage treatment process contains many pathogenic bacteria, which will impact patients and surrounding residents. In this study, the biochemical tank (BRT) of the hospital sewage treatment station (HSTS) and municipal wastewater treatment plant (MWTP) were used as sampling points. The results showed that the concentration of bacteria (1843 CFU/m³) in bioaerosol produced by BRT of HSTS was higher than that in the air at BRT of MWTP (1278 CFU/m³). The proportion of small-size bacteria (<3.3 µm) in the air of HSTS and MWTP was similar. However, the abundance of small-size pathogenic bacteria in HSTS was higher than that in MWTP, such as Acinetobacter and Arcobacter. The dominant bacteria in HSTS and MWTP were different under different particle sizes. The dominant bacterial genera of bioaerosol in HSTS under different particle sizes were similar (Acinetobacter, Arcobacter, Comamonas); There were significant differences in the dominant bacterial genera of bioaerosol in MWTP under different particle sizes. The dominant strains with particle sizes ranging from 0 ∼ 0.43 µm were Acinetobacter (23.22%). Kocuria (15.13%) accounted for a relatively high proportion in the aerosol of 0.43 µm ∼ 0.65 µm. The dominant strains with particle sizes of 0.65 µm ∼ 1.1 µm and 1.1 µm ∼ 2.1 µm were relatively single, and Exiguobacterium and Paenibacillus accounted for 51.51% and 60.15%, respectively. Source tracker showed that most of the pathogenic bacteria in bioaerosols came from sewage. One hour later, the concentration of particulate matter in the place 200 m away from BRT of HSTS (1 × 10^-10 mg/m³) was higher than that in MWTP (1 × 10^-11 mg/m³). The hazard quotient (HQ) of people around HSTS (HQ_male: 1.70 × 10^-1; HQ_female: 1.36 × 10^-1) was higher than that of MWTP (HQ_male: 1.18 × 10^-1; HQ_female: 9.40 × 10^-2). Pathogenic bacteria (Acinetobacter, Arcobacter) were detected in HSTS and MWTP and the BugBase phenotype prediction results showed potential pathogenicity. More attention should be paid to the protection of the people. It is suggested to strengthen the air sterilization treatment near HSTS according to the diffusion trajectory of bioaerosol, and the surrounding personnel should wear N95 and other protective masks.

[The postal code as a "bar code" of antimicrobial resistance]

OBJECTIVE

The need to integrate local resistances into clinical practice is increasingly urgent, especially in Primary Care where empirical treatment is frequent.

METHODS

A retrospective observational study of positive microbiological isolates of Neisseria gonorrhoeae from any location (urethral, cervical, pharyngeal, rectal or urine) was carried out in the health area of Alcalá de Henares. Sociodemographic characteristics and resistance to cephalosporins, azithromycin, penicillin and quinolones were analyzed. Each isolate was related to its postal code of origin.

RESULTS

We analyzed 256 microbiological samples of N.gonorrhoeae, most of them male (92.9%) with a mean age of 33 years. Half of the samples (49.8%) were resistant to ciprofloxacin. Temporal and spatial evolution of antimicrobial resistance was integrated in heat maps.

CONCLUSIONS

Knowing local resistances can help to prescribe more adequate empirical treatments, especially in Primary Care, avoiding inadequate antibiotics and decreasing resistance rates.

A heterogenic membrane-based biomimetic hybrid nanoplatform for combining radiotherapy and immunotherapy against breast cancer

Radiotherapy is adopted to obliterate multiple malignant tumors clinically, which might also induce antitumor immune response. However, traditional radiotherapy is not enough to ablate tumors and activate long-term immunological response. Here, we developed a hybrid nanoplatform (MGTe) composed of GTe (glutathione (GSH) decorated Te nanoparticles) and fusing tumor cell membranes (TM) and bacterial outer membranes (BM). In this nanoplatform, GTe was designed for radiotherapy sensitization, concurrently the fusion of TM and BM was expected for amplifying antitumor immune. With a high-Z element, MGTe could enhance radiosensitivity by reactive oxygen species (ROS) production and cancer cell immunogenic death (ICD) under X-ray irradiation, which would also trigger antitumor immune. At meanwhile, TM and BM would further enlarge the immunological effects through antigen presenting cells (APCs) maturation and cytotoxic T lymphocytes (CTLs) stimulation. In this synergistic strategy, the combination of MGTe and X-ray showed significant tumor inhibition by radiation-driven immunotherapy, which will find great potential as an attractive clinical alternative to fight against tumor with reduced side effects.

Diversity of fungi and bacteria in bronchoalveolar lavage fluid during development of chronic obstructive pulmonary disease

The dynamic changes in microbiome during chronic obstructive pulmonary disease (COPD) exacerbations remains unclear. Using 16S ribosomal DNA and fungal internal transcribed spacer DNA sequencing, we described the composition and changes in the bacterial and fungal microbiota of bronchoalveolar lavage fluid (BALF) samples from 15 COPD patients and 7 non-COPD patients. In COPD patients, the dominant bacteria phyla were Proteobacteria, Firmicutes, Bacteroidete and Actinobacteria. The most abundant fungal phyla were Ascomycota and Basidiomycota. In terms of the genera of the bacteria and fungi, the numbers of Veillonella, Prevotella-7, Haemophilus, and Aspergillus were significantly more in COPD compared with the non-COPD patients. In addition, after the progression of COPD, the relative abundances of fungal genera of Aspergillus, Mortierella, Grifola, Thermoascus, Russula, and Thermomyces and the bacteria genera of Proteobacteria increased significantly. Existing analyses demonstrate changes in the diversity of bacterial and fungal communities, which appeared to be related to COPD. Our results demonstrated the potential utility of the microbiota as possible biomarkers for disease progression and provided therapeutic targets for COPD.

Microbiological Profile of Ocular Infection: A Large Retrospective Study

BACKGROUND

We aimed to elucidate the pathogenic bacterial and fungal profiles of specimens obtained from suspected ocular infections at Farabi Eye Tertiary Referral Hospital, Tehran, Iran.

METHODS

In this cross-sectional study, we collected data from ocular specimens taken during the seven-year period of 2011 to 2018, and the results were then retrospectively analyzed. Samples had been obtained from patients who were investigated for ocular infections.

RESULTS

Overall, 16,656 ocular samples were evaluated. The mean patient age was 48.31 ± 26.62 years. Most patients were men (60.33%), and men in the 7th decade of life were the largest represented group. The seasonal distributions of specimen collection sites followed the overall distribution of collection sites by year. Specimens obtained from the cornea were the most common (49.24%), also representing the largest number of specimens in all seasons. The most commonly isolated fungal microorganisms were Fusarium spp., followed by Aspergillus spp. and Candida albicans. Of the 6,556 specimens with positive bacterial cultures, 59% produced gram-positive bacteria, while the remainder produced gram-negative pathogens. The most commonly isolated bacteria were Pseudomonas aeruginosa (17.77%), Staphylococcus epidermidis (13.80%), Streptococcus pneumoniae (13.27%), S. viridans (12.23%), and S. aureus (11.18%).

CONCLUSION

Most submitted specimens were obtained from the cornea. The most commonly isolated fungal microorganisms were Fusarium spp., followed by Aspergillus spp. and C. albicans. The most commonly isolated bacteria were P. aeruginosa, followed by S. epidermidis and S. pneumoniae.

COVID-19 cases and their outcome among patients with uncommon co-existing illnesses: A lesson from Northern India

Introduction

Newer coexisting conditions should be identified in order to modify newer risk factors. Aim was to identify patients with non-classical or less common coexisting conditions in patients infected of COVID 19.

Method

Single centred study from June 2020 to May 2021 at a tertiary centre in North India. A preformed questionnaire was used to record clinical and laboratory parameters and to identify cases which are in addition to CDC list and Indian data.

Results

0.67% (46) cases out of 6832 patients were identified to have non-classical coexisting illness. It was divided into 2 groups-infections A (60.1%) and non-infections B (39.9%). Group A included-tuberculosis- pulmonary (14.3%) & extra pulmonary (32.9%), bacterial (25.0%) viral infections [dengue, hepatitis B & C] (14.3%), HIV disease (10.7%) and malaria (3.6%). Group B included- organ transplant (27.8%), autoimmune [myasthenia gravis, polymyositis, psoriasis] (22.6%), haematologic [Haemophilia, ITP, Aplastic anaemia, APML, CML] (27.8%), uncommon malignancies [disseminated sacral chordoma and GTN] (11.1%) and snakebite (11.1%). Serum Procalcitonin was not helpful for diagnosis of bacterial infection in COVID-19 disease. Group A had significantly longer duration of illness, hepatitis and elevated CRP. The mortality in group A & B were 32.1% and 43.8% respectively. Death in non-severe COVID cases was in tetanus and snakebite. 30.7% death among tuberculosis patients. More than 70% of deaths were attributable to COVID 19 in both the groups.

Conclusion

In Indian settings, comorbidities like tuberculosis and bacterial infections can precipitate severe COVID 19 unlike other parts of the world where tuberculosis is relatively uncommon.

Optimizing antibiotic therapies to reduce the risk of bacterial resistance

The incidence of infections caused by bacteria that are resistant to antibiotics is constantly increasing. In Europe alone, it has been estimated that each year about 33'000 deaths are attributable to such infections. One important driver of antimicrobial resistance is the use and abuse of antibiotics in human medicine. Inappropriate prescribing of antibiotics is still very frequent: up to 50% of all antimicrobials prescribed in humans might be unnecessary and several studies show that at least 50% of antibiotic treatments are inadequate, depending on the setting. Possible strategies to optimize antibiotic use in everyday clinical practice and to reduce the risk of inducing bacterial resistance include: the implementation of rapid microbiological diagnostics for identification and antimicrobial susceptibility testing, the use of inflammation markers to guide initiation and duration of therapies, the reduction of standard durations of antibiotic courses, the individualization of antibiotic therapies and dosing considering pharmacokinetics/pharmacodynamics targets, and avoiding antibiotic classes carrying a higher risk for induction of bacterial resistance. Importantly, measures to improve antibiotic prescribing and antibiotic stewardship programs should focus on facilitating clinical reasoning and improving prescribing environment in order to remove any barriers to good prescribing.

Effect of TiO2 on Selected Pathogenic and Opportunistic Intestinal Bacteria

Food-grade titanium dioxide (TiO₂) containing a nanoparticle fraction (TiO₂ NPs-nanoparticles) is widely used as a food additive (E171 in the EU). In recent years, questions concerning its effect on the gastrointestinal microbiota have been raised. In the present study, we examined interactions between bacteria and TiO₂. The study involved six pathogenic/opportunistic bacterial strains and four different-sized TiO₂ types: three types of food-grade E171 compounds and TiO₂ NPs (21 nm). Each bacterial strain was exposed to four concentrations of TiO₂ (60, 150, 300, and 600 mg/L TiO₂). The differences in the growth of the analyzed strains, caused by the type and concentration of TiO₂, were observed. The growth of a majority of the strains was shown to be inhibited after exposure to 300 and 600 mg/L of the food-grade E171 and TiO₂ NPs.

High mortality from carbapenem-resistant Klebsiella pneumoniae bloodstream infection

In this study, it was evaluated clinical data of 107 patients with bloodstream infection (BSI) by Klebsiella pneumoniae and performed phenotypic and molecular analyzes in 50.5% (54/107) of the samples, those that showed a resistance profile to carbapenemics. The bla_KPC gene was present in 90.4% (49/54) of the samples, bla_NDM gene in one sample and, in 7.4% (4/54) of the samples, no carbapenemase gene was found. In the similarity analysis, it was found 4 main clones and 11 samples were not genetically related. The median age of the patients was 58 (40-70) years old and 60.7% (65/107) were male. When comparing two groups of patients with BSI due to K. pneumoniae with and without resistance to carbapenems, the variables ICU permanence, renal failure (IR), previous use of antimicrobials, Charlson's comorbidity index (ICCi), some invasive procedures and death showed a statistically significant difference (p < 0.05). And when relating death as a dependent variable, IR, liver failure and patients with BSI XDR or PDR, were predictors of increased mortality. Our study showed a higher mortality rate in patients with BSI due to carbapenem-resistant pneumonia with additional resistance or not to polymyxins.

Outcome of Adult Malarial Co-infections in Eastern India

Introduction:

Co-infection with different agents such as bacterial, viral, and Rickettsia is being increasingly recognized due to greater availability and utilization of the diagnostic tests among malaria patients.

Methods:

Consecutive admitted malarial cases were included and were subjected to test for general investigations, bacteria, typhoid, dengue, chikungunya, and rest for specific diagnosis. All patients were followed up till discharge or death and appropriate statistical tests were performed.

Results:

A total of 152 malaria patients were recruited and 27 (18.8%) had concurrent infections. It included 40.7% dengue only, 18.7% pneumonia, 11.1% urinary tract infection (UTI), 7.4% enteric fever, 3.7% leptospirosis, chikungunya, and tuberculous meningitis each, and 3.7% each of dengue with pneumonia and UTI. The organisms isolated were Streptococcus pneumoniae, Klebsiella pneumoniae, Escherichia coli, Salmonella typhi, and Mycobacterium tuberculosis. The mean duration of fever was 6.33 ± 3.63 days with a range of 3–20 days. Blood culture grew in 2 cases S. typhi and K. pneumonia,e. Dengue co-infections had significantly higher clinical and laboratory features of dengue and complications such as bleeding, jaundice, and cholecystitis, whereas rest concurrent infections had a significantly higher proportion of nausea and vomiting, convulsion, altered sensorium, productive cough, urinary symptoms, shock, acute kidney injury, anemia, and mean neutrophil count. There was significantly higher mortality among malaria–dengue concurrent infection group with 2 (15.4%) than malaria mono-infection group 3 (2.4%).

Conclusion:

Co-infections with malaria are not uncommon, especially dengue fever and other bacterial infections. The dominant clinical picture is of the superimposed infection. Decision should be clinically guided adjunct with specific diagnostic tests, and timely treatment has favorable outcome.

Blood bacterial resistant investigation collaborative system (BRICS) report: a national surveillance in China from 2014 to 2019

BACKGROUND

In this first national bloodstream infection (BSI) surveillance program in China, we assessed the composition of pathogenic bacteria and the trends for antimicrobial susceptibility over a 6-year period in China.

METHODS

Blood bacterial isolates from patients at hospitals participating in the Blood Bacterial Resistant Investigation Collaborative System (BRICS) were collected from January 2014 to December 2019. Only the first isolate of a species per patient was eligible over the full study period. Antibiotic-susceptibility testing was conducted by agar-dilution or broth-dilution methods as recommended by the Clinical and Laboratory Standards Institute (CLSI). WHONET 5.6 was used to analyze data.

RESULTS

During the study period, 27,899 bacterial strains were collected. Gram-positive organisms accounted for 29.5% (8244) of the species identified and Gram-negative organisms accounted for 70.5% (19,655). The most-commonly isolated organisms in blood cultures were Escherichia coli, Klebsiella pneumoniae, Staphylococcus aureus, coagulase-negative Staphylococci, and Acinetobacter baumannii. The prevalence of multidrug-resistant organisms, such as E. coli, K. pneumoniae, A. baumannii was higher in tertiary hospitals, whereas extended-spectrum, β-lactamase-producing E. coli (ESBL-E. coli), carbapenem-resistant A. baumannii were more prevalent in economically-developing areas. The prevalence of methicillin-resistant S. aureus declined from 39.0% (73/187) in 2014 to 25.9% (230/889) in 2019 (p < 0.05). The prevalence of ESBL-E. coli dropped from 61.2% (412/673) to 51.0% (1878/3,683) over time (p < 0.05), and carbapenem-resistant E. coli remained low prevalence (< 2%; 145/9944; p = 0.397). In contrast, carbapenem-resistant K. pneumoniae increased markedly from 7.0% (16/229) in 2014 to 19.6% (325/1,655) in 2019 (p < 0.05).

CONCLUSION

E. coli and K. pneumoniae were the leading causes of BSI during the 6-year study period. The major resistant pathogens declined or remained stable, whereas carbapenem-resistant K. pneumoniae continued to increase, which poses a great therapeutic challenge for BSIs.